Razib Khan One-stop-shopping for all of my content

November 20, 2013

Our ancestors are part us…or the other way around?

Filed under: Archaeology,Siberian boy — Razib Khan @ 11:34 am

Keeping a close watch on media representations of the new Nature paper on the ancient Siberian genome. Here’s The New York Times, 24,000-Year-Old Body Is Kin to Both Europeans and American Indians. I don’t have a problem with the title, but the roll-out isn’t totally accurate in what it will connote to the audience in my opinion:

he genome of a young boy buried at Mal’ta near Lake Baikal in eastern Siberia some 24,000 years ago has turned Tout to hold two surprises for anthropologists.

The first is that the boy’s DNA matches that of Western Europeans, showing that during the last Ice Age people from Europe had reached farther east across Eurasia than previously supposed. Though none of the Mal’ta boy’s skin or hair survive, his genes suggest he would have had brown hair, brown eyes and freckled skin.

The second surprise is that his DNA also matches a large proportion — some 25 percent — of the DNA of living Native Americans. The first people to arrive in the Americas have long been assumed to have descended from Siberian populations related to East Asians. It now seems that they may be a mixture between the Western Europeans who had reached Siberia and an East Asian population.

The Mal’ta boy was aged 3 to 4 and was buried under a stone slab wearing an ivory diadem, a bead necklace and a bird-shaped pendant. Elsewhere at the same site some 30 Venus figurines were found of the kind produced by the Upper Paleolithic cultures of Europe. The remains were excavated by Russian archaeologists over a 20-year period ending in 1958 and stored in museums in St. Petersburg.

The issue I have is that modern Europeans are a new population which emerged through admixture processes over the past ~10,000 years. And one of those populations which contributed to their ancestry are the descendants of the Siberian boy! Talking about “Western Europeans” ~20,000 years ago is geographic convenience. They wouldn’t be “Western Europeans” as we understand them genetically. Even if there wasn’t any recent admixture, ~1,000 generations of drift is not trivial. Though the archaeology may clarify, I also don’t think it is definite that the ancient Siberians were from Europe as we’d understand it. Perhaps they all come from a common Central Eurasian stock which diversified?

Not that I have a better solution for terminology.

The post Our ancestors are part us…or the other way around? appeared first on Gene Expression.

The long First Age of mankind

Filed under: Anthroplogy,Archaeology,Siberians — Razib Khan @ 10:22 am

OldSiberian

“What it begins to suggest is that we’re looking at a ‘Lord of the Rings’-type world – that there were many hominid populations,” says Mark Thomas, an evolutionary geneticist at University College London who was at the meeting but was not involved in the work.

- Mark Thomas, as reported by Nature

This is in reference to the ancient DNA meeting where David Reich reported that the Denisovans, an exotic archaic population which contributed ~5-10 percent of the ancestry of Papuans, was itself a synthesis of Neandertals and a mysterious group currently unknown. This is not surprising, as the broad outlines of these results were presented at ASHG 2012, though no doubt they’re moving closer to publication. But for this post I want to shift the focus to a different time and place, after the ancient admixture with archaic lineages, and to the reticulation present within our own.


But first we need to backtrack a bit. Let’s think about what we knew in the early 2000s. If you want a refresher, you might check our Spencer Wells’ The Journey of Man or Stephen Oppeneheimer’s Out of Eden, which focused on Y and mtDNA lineages respectively. These books were capstones to the era of uniparental phylogeographic analysis of the spread and diversification of anatomically modern African hominids ~50-100,000 years ago. Rather than looking at the whole genome (the technology was not there yet) these researchers focused on pieces of DNA passed down via direct maternal or paternal lineages, and reconstructed clean phylogenetic trees using a coalescent framework. Broadly speaking these trees were concordant, and told us that our lineage, all extant humans, derived from a small African population which flourished ~100,000 years ago. These insights suffused the thought of human evolutionary thinkers in other disciplines (see The Dawn of Human Culture). H. sapiens sapiens, veni, vidi, vici.

After that initial “Out of Africa” migration a series of bottlenecks and founder events led to the expansion of our lineage, as it replaced all predecessors. By the Last Glacial Maximum, ~20-25,000 years ago, the rough outlines of human genetic variation were established (with the exception of the expansion into the New World). We know now that this picture is very incomplete at the most innocuous, and highly misleading given the least charitable interpretation.

Reticulation. Graphs. Admixture. These words all point to the reality that rather than being the culmination of deep rooted regional populations which date back to the depths of the Pleistocene, most modern humans are recombinations of ancient lineages. On the grandest scale this is illustrated by the evidence of ‘archaic’ ancestry in modern humans. But even more pervasively we see evidence of widespread admixture between distinct lineages which are major world populations which we think of as archetypes. This is true for Amerindians, South Asians, and Europeans. This is also the case for Ethiopians, and Australian populations. A major problem crops up when we talk about extinct ancient populations which were the founding substituent elements of modern ones: it doesn’t make sense to use modern referents when they are simply recombinations of what they are describing. But language and history being what they weare we can’t change the awkwardness of talking about “Ancestral North Eurasians,” anodyne and somewhat incoherent at the same time (Eurasia is a modern construct with contemporary historical salience).

Into the mix comes another ancient DNA paper which reconstructs the genome of a boy who lived in Siberia, near Lake Baikal, somewhat over 20,000 years ago. It’s titled Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Here’s the topline finding: a substantial minority of the ancestry of modern Native Americans derives from a North Eurasian population which has closer affinities to West Eurasians than East Eurasians. And, this is an old admixture event. In the paper itself they observe that all “First American” populations seem to exhibit the same admixture distance to the Siberian genome. These results are also broadly consistent with the admixture of this population in Western Eurasia, especially northeast Europe. As among Amerindian populations it seems that this element is at substantial minority across Europe as a whole, and perhaps at parity in some populations, such as Finns.

Fig1To the left you see the geographical affinities of the MA-1 Siberian sample. It is shifted toward West Eurasians in the PCA. But on the map with circles representing populations, the definite evidence of admixture between Amerindians and MA-1 is clear in the shading. The statistic used, f-3, looks for complex population history between and outgroup (X) and a putative clade. From this test it is evident Amerindians had some admixture related to MA-1. Because of the dating of Siberian remains it does not seem likely that admixture was from Amerindians to West Eurasian and related populations. Rather, the reverse seems more plausible. You can also see from the map the close affinities with particular European and Central Asian populations of MA-1. This is intriguing, and requires further follow up. Though MA-1 and its kin were closer to West Eurasians than East Eurasians, it still seems likely that there was an early divergence between the populations of north-northeast Eurasia, and those of the southwest. Eventually they came back together in various proportions to produce modern Europeans, but it seems likely that during the Pleistocene these two groups went their own way.

treemixThere are hints of this in the TreeMix plot to the right. Note now drifted MA-1 is in relation to other West Eurasians (the branch is long). I suspect some of this is due to the fact that this individual is nearly 1,000 generations in the past. Not only is it difficult to name ancient populations with those of moderns, I suspect that some of the variation in the ancient populations has been lost, and so they seem exotic and difficult to fit into a broader phylogenetic framework (they had hundreds of thousands of SNPs though). And yet MA-1 can be fitted into the broader framework of populations which went north or west after leaving Africa because of mtDNA and Y chromosome results. Both of these indicate that MA-1 was basal to West Eurasians, with haplogroup U for mtDNA, and R for the Y lineage.

To really understand what’s going on here is going to take a while. A later subfossil, circa ~15,000 years before the present, yielded some genetic material, and exhibited continuity with MA-1. This suggests that Siberia may have had massive population replacement relatively recently. We know this was likely the case elsewhere. Reading Jean Manco’s Ancestral Journeys one possible scenario is that Pleistocene Europeans were MA-1 like, but were replaced by Middle Eastern farmers in the early Neolithic. But later eruptions from Central Asia brought mixed populations (Indo-Europeans?) with substantial MA-1 affinities to the center of European history.

Finally, one must make a note of phenotype. The authors looked at 124 pigmentation related SNPs (see supplemental). The conclusion seems to be that MA-1 was not highly de-pigmented, as is the case with most modern Northern Europeans. This stands to some reason, as substantial ancestry of this sort in Amerindians would result in phenotypic variation which does not seem to be present. Though the authors do suggest that coarse morphological variation among early First Americans (e.g., Kennewick Man) might be due to this population, which had West Eurasian affinities.

Where does this leave us? More questions of course. Though I’m confident the befuddlement will clear up in a few years….

Citation: doi:10.1038/nature12736

Addendum: Please read the supplements. They’re rich enough that you don’t need to read the letter if you don’t have access. Also, can we now finally bury the debate when east and west Eurasians diverged? Obviously it can’t have been that recent if a >20,000 year old individual had closer affinity to western populations.

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October 30, 2013

The human genetic casserole

Filed under: Archaeology,Human History — Razib Khan @ 6:48 pm

HotdishI haven’t said much about this article in Science, Ancient DNA Links Native Americans With Europe, because it would be an understatement to say I’m digesting it. I would offer up a caution that using terms like “Europeans” and “East Asians” for populations which flourished ~25,000 years ago might be misleading. We are used to thinking of genetic distance in terms of space, but time is also a dimension to consider. Populations even without admixture or gene flow will have drifted in allele frequencies over so many generations.

But I have to admit that it seems more and more likely that most extant modern populations are combinations of lineages which diverged very early after the “Out of Africa” migration. We see this clearly with South Asians, and now Europeans and Native Americans. The Reich lab has also found evidence of admixture in in Australians. The closer we look, the more amalgamation we see between disparate lineages. Using the elements of the present to reconstruct the patterns of the past is going to be a more daunting task than most would have guessed.

The post The human genetic casserole appeared first on Gene Expression.

November 17, 2012

The archaeologist, James Fallows, and Neandertals

Filed under: Anthroplogy,Archaeology,Genetics,Neandertals — Razib Khan @ 10:10 pm

A month ago I posted Don’t trust an archaeologist about genetics, don’t trust a geneticist about archaeology, in response to James Fallows at At 5% Neanderthal, You Are an Outlier. Fallows has now put up a follow up, The Neanderthal Defense Committee Swings Into Action, where he links to my response post. This prompted the original archaeologist in question to reach out to me via email. I am posting the letter, with their permission, below.

Hello!

I’m dropping an email because I followed a link from Fallows to find my email to him highlighted negatively on your blog. I’ve emailed a few times with Mr. Fallows on various topics and had no idea he was going to post that email – he didn’t ask until after it was already up and so, yes you’re right it was a casual dashed off email and confused two different articles (both of which incidentally I have read so please no more comments on what I may or may not have done). Mea Culpa. And you’re right, I’m not a geneticist – I’m not even a lab scientist. However, I know a heck of a lot about archaeology and I work closely with ...

July 12, 2012

The past as a cultural landscape

Filed under: Anthroplogy,Archaeology,Native Americans — Razib Khan @ 9:03 pm

By now you have read that the Clovis people may have had contemporaries. In case you didn’t know, until about ~10 years the “standard model” of the peopling of the Americas was that around ~13,000 years ago one single population crossed into the New World via Beringia, and rapidly swept north to south in ~1,000 years. These were the Clovis people, associated with a particular toolkit, and perhaps implicated in megafaunal extinctions. Today this model is no longer held to be sacrosanct, though no clear successor has emerged. It does seem likely that some sort of pre-Clovis population is presumed to exist. These data are interesting because they indicate that there may have been geographical structure in cultural forms even at this early stage in North America, implying that the original peopling of America was not homogeneous. That is, there may have been several founding groups.

I find this entirely plausible. It strikes me that a fear years ago a tendency toward rhetorical extremism occasionally found purchase when it came to the settlement of the peripheries of the human range, Oceania and the New World. Jared Diamond famously proposed that ...

May 15, 2011

Genetic variation in the Caucasus

The Pith: There is a very tight correlation between language and genes in the Caucasus region.

If the Soviet Union was the “The Prisonhouse of Nations,” then the Caucasus region must be the refuge of the languages. Not only is this region linguistically diverse on a fine-grained scale, but there are multiple broader language families which are found nowhere else in the world. The widespread Indo-European languages are represented by Armenians, Greeks, and Iranians. The similarly expansive Altaic languages are represented by the Turkic dialects. But in addition to these well known groups which span Eurasia there are the Northwest Caucasian, Northeast Caucasian, and Kartvelian, families. These have only a local distribution despite their distinctiveness.

On the one hand we probably shouldn’t be that surprised by the prominence of small and diverse language families in this rugged region between Russia and the Near East. Mountains often serve as the last refuges of peoples and cultures being submerged elsewhere. For example, in the mountains of northern Pakistan you have the linguistic isolate of Burusho, which has no known affinity with other languages. Likely it once had relatives, but they were assimilated, leaving only ...

February 2, 2011

Empires and Barbarians: The Fall of Rome and the Birth of Europe

Link to review: Say it with me: Völkerwanderung

December 13, 2010

Live not by visualization alone

pc1
Synthetic map

In the age of 500,000 SNP studies of genetic variation across dozens of populations obviously we’re a bit beyond lists of ABO blood frequencies. There’s no real way that a conventional human is going to be able to discern patterns of correlated allele frequency variations which point to between population genetic differences on this scale of marker density. So you rely on techniques which extract the general patterns out of the data, and present them to you in a human-comprehensible format. But, there’s an unfortunate tendency for humans to imbue the products of technique with a particular authority which they always should not have.

ResearchBlogging.orgThe History and Geography of Human Genes is arguably the most important historical genetics work of the past generation. It has surely influenced many within the field of genetics, and because of its voluminous elegant visual displays of genetic data it is also a primary source for those outside of genetics to make sense of phylogenetic relations between human populations. And yet one aspect of this great work which never caught on was the utilization of “synthetic maps” to visualize components of genetic variation between populations. This may have been fortuitous, a few years ago a paper was published, Interpreting principal components analyses of spatial population genetic variation, which suggested that the gradients you see on the map above may be artifacts:

Nearly 30 years ago, Cavalli-Sforza et al. pioneered the use of principal component analysis (PCA) in population genetics and used PCA to produce maps summarizing human genetic variation across continental regions. They interpreted gradient and wave patterns in these maps as signatures of specific migration events. These interpretations have been controversial, but influential, and the use of PCA has become widespread in analysis of population genetics data. However, the behavior of PCA for genetic data showing continuous spatial variation, such as might exist within human continental groups, has been less well characterized. Here, we find that gradients and waves observed in Cavalli-Sforza et al.’s maps resemble sinusoidal mathematical artifacts that arise generally when PCA is applied to spatial data, implying that the patterns do not necessarily reflect specific migration events. Our findings aid interpretation of PCA results and suggest how PCA can help correct for continuous population structure in association studies.

A paper earlier this year took the earlier work further and used a series of simulations to show how the nature of the gradients varied. In light of recent preoccupations the results are of interest. Principal Component Analysis under Population Genetic Models of Range Expansion and Admixture:

In a series of highly influential publications, Cavalli-Sforza and colleagues used principal component (PC) analysis to produce maps depicting how human genetic diversity varies across geographic space. Within Europe, the first axis of variation (PC1) was interpreted as evidence for the demic diffusion model of agriculture, in which farmers expanded from the Near East ∼10,000 years ago and replaced the resident hunter-gatherer populations with little or no interbreeding. These interpretations of the PC maps have been recently questioned as the original results can be reproduced under models of spatially covarying allele frequencies without any expansion. Here, we study PC maps for data simulated under models of range expansion and admixture. Our simulations include a spatially realistic model of Neolithic farmer expansion and assume various levels of interbreeding between farmer and resident hunter-gatherer populations. An important result is that under a broad range of conditions, the gradients in PC1 maps are oriented along a direction perpendicular to the axis of the expansion, rather than along the same axis as the expansion. We propose that this surprising pattern is an outcome of the “allele surfing” phenomenon, which creates sectors of high allele-frequency differentiation that align perpendicular to the direction of the expansion.

The first figure shows the general framework with which they performed the simulations:

pcab1

You have a lattice which consists of demes, population units, all across Europe. They modulated parameters such as population growth (r), carrying capacity (C), and migration (m). Additionally, they had various scenarios of expansion from the southwest or southeast, as well as two expansions one after another to mimic the re-population of Europe after the Ice Age by Paleolithic groups, and their later replacement by Neolithic groups. They modulated admixture and introgression of genes from the Paleolithic group to the Neolithics so that you had the full range where the final European were mostly Neolithic or mostly Paleolithic.

Below are some of the figures which show the results:

allesurAs you can see the strange thing is that in some models the synthetic map gradient is rotated 90 degrees from the axis of demographic expansion! In this telling the famous synthetic map showing Neolithic expansion might be showing expansion from Iberia. Perhaps a radiation from a post-Ice Age southern refuge?

One explanation might be “allele surfing” on the demographic “wave of advance.” Basically as a population expands very rapidly stochastic forces such as random genetic drift and bottlenecks could produce diversification along the edge of the population wave front. The reason for this is that these rapidly expanding populations explode out of serial bottlenecks and demographic expansions, which will produce genetic distinctiveness among the many differentiated demes bubbling along the edge of expansion. Alleles which may have been at low frequency in the ancestral population can “fix” in descendant populations on the edge of the demographic wave of advance. This is the explanation, more or less, that one group gave last year for the very high frequencies of R1b1b2 in Western Europe. With this, they overturned the classic assumption that R1b1b2 was a Paleolithic marker, and suggested it was a Neolithic one.

Here’s their conclusion from the paper:

A previous study showed that the original patterns observed in PCA might not reflect any expansion events (Novembre and Stephens 2008). Here, we find that under very general conditions, the pattern of molecular diversity produced by an expansion may be different than what was expected in the literature. In particular, we find conditions where an expansion of Neolithic farmers from the southeast produces a greatest axis of differentiation running from the southwest to the northeast. This surprising result is seemingly due to allele surfing leading to sectors that create differentiation perpendicular to the expansion axis. Although a lot of our results can be explained by the surfing phenomenon, some interesting questions remain open. For example, the phase transition observed for relatively small admixture rates between Paleolithic resident and Neolithic migrant populations occurs at a value that is dependent on our simulation settings, and further investigations would be needed to better characterize this critical value as a function of all the model parameters. Another unsolved question is to know why the patterns generally observed in PC2 maps for our simulation settings sometimes arise in PC1 maps instead. These unexplained examples remind us that PCA is summarizing patterns of variation in the sample due to multiple factors (ancestral expansions and admixture, ongoing limited migration, habitat boundary effects, and the spatial distribution of samples). In complex models such as our expansion models with admixture in Europe, it may be difficult to tease apart what processes give rise to any particular PCA pattern. Our study emphasizes that PC (and AM) should be viewed as tools for exploring the data but that the reverse process of interpreting PC and AM maps in terms of past routes of migration remains a complicated exercise. Additional analyses—with more explicit demographic models—are more than ever essential to discriminate between multiple explanations available for the patterns observed in PC and AM maps. We speculate that methods exploiting the signature of alleles that have undergone surfing may be a powerful approach to study range expansions.

What’s the big picture here? In the textbook Human Evolutionary Genetics it is asserted that synthetic maps never became very popular compared to PCA itself. I think this is correct. But, the original synthetic maps have become prominent for many outside of genetics. They figure in Peter Bellwood’s First Farmers, and are taken as a given by many pre-historians, such as Colin Renfrew. And yet a reliance on these sorts of tools must not be blind to the reality that the more layers of abstraction you put between your perception and comprehension of concrete reality, the more likely you are to be led astray by quirks and biases of method.

In this case I do think first-order intuition would tell us that synthetic maps which display PCs would be showing gradients as a function of demographic pulses. And yet the intuition may not be right, and with the overturning of old orthodoxies in the past generation of inferences from the variation patterns in modern populations, we should be very cautious.

Citation: Olivier François, Mathias Currat, Nicolas Ray, Eunjung Han, Laurent Excoffier, & John Novembre (2010). Principal Component Analysis under Population Genetic
Models of Range Expansion and Admixture Mol Biol Evol

December 3, 2010

The great northern culture war

A new paper in The New Journal of Physics shows that a relatively simple mathematical model can explain the rate of expansion of agriculture across Europe, Anisotropic dispersion, space competition and the slowdown of the Neolithic transition:

The front speed of the Neolithic (farmer) spread in Europe decreased as it reached Northern latitudes, where the Mesolithic (hunter-gatherer) population density was higher. Here, we describe a reaction–diffusion model with (i) an anisotropic dispersion kernel depending on the Mesolithic population density gradient and (ii) a modified population growth equation. Both effects are related to the space available for the Neolithic population. The model is able to explain the slowdown of the Neolithic front as observed from archaeological data

The paper is open access, so if you want more of this:
fareq

Just click through above. Rather, I am curious more about their nice visualization of the archaeological data:


euroneolithic

Note how much variance there is in terms of the rate of change of the clines. As I’ve observed before there was a “break out” of the LBK farmers into Central Europe nearly 7,000 years ago, but it took much longer to close the gap between the farms on the frontier and the sea. This is well known from the archaeology, as there seems to have been a pause of ~1,000 years across much of the north European plain. On the scale of 10,000 years that’s not much time, but that’s about 40 generations. In Frisia it looks like the spreading of farming stopped for nearly ~2000 years!

Why the abatement of the spread of farming? I think the authors of the above paper are correct in their acceptance of the conventional wisdom of greater Mesolithic densities in Northern Europe. But I think perhaps a better description might be maritime Northern Europe. We often imagine early farmers displacing hunters and gatherers of game and herb, but what if in much of the world the main clash numerically was between dense populations oriented toward the sea, and those who were depended on the land? About seven years ago a study came out which argued for a rapid transition from seafood to meat in the diets of early Britons, Why Did Ancient Britons Stop Eating Fish?:

When cattle, sheep, pigs, and wheat arrived on the shores of Great Britain about 5,000 years ago, fish quickly fell off the Neolithic menu, according to an analysis of human bones scattered throughout the island.

“Farming really took off in Britain during the Neolithic. The main questions concerning the speed of change relates to how quickly Mesolithic peoples adapted—or otherwise—to the new farming methods and/or the spread of farming into Britain by new farming communities,” he said.

The research by Richards and colleagues Rick Schulting at Queen’s University Belfast and Robert Hedges at the University of Oxford tracks the shift in diet by examining the dietary signature stored in the bones.

They find that the shift was rapid and complete at the onset of the Neolithic. “Marine foods, for whatever reason, seem to have been comprehensively abandoned,” the researchers conclude in the September 25 issue of the journalNature.

“We determined that after the introduction of domesticates, as well as the other artifacts associated with the Neolithic, the isotope values showed that marine foods were not used anymore,” he said. “We then infer that this is a switch from wild foods such as fish and shellfish to the new domesticates that arrive at this time.”

Richards said there are three plausible reasons why the British abandoned seafood from the beginning of the Neolithic: the domesticated plants and animals presented a steady source of food; the shift was forced by a climate change; or cultural pressure.

In the early 2000s the idea of wholesale rapid demographic replacement was not in the air. I think we need to put that back on the table. Here is the chart on isotope ratios from the 2003 paper:
culwar

Notice the sharp discontinuity. Richards et al. in 2003 interpreted this as a rapid cultural acquisition of the Neolithic lifestyle ~2500-3000 BC. They note in the media reports that later Britons, for example at the time of the Roman conquest, seem to have utilized fish a bit more in their diet than these early Neolithics. This stands to reason, much of Britain is not too far from the sea. To me the very sharp drop in marine consumption is indicative more of a food taboo, than a practical shift. Obviously farmers would primarily be subsistent on grain, but there’s no necessary reason to avoid meat or fish, but as it happens in many parts of the world societies preserve and perpetuate exactly such norms. These norms may have spread through cultural diffusion, for example through an adoption of a new religion. Or, the norms may have been brought by a new group which arrived in large numbers and replaced the indigenous population.

Here is an equivalent chart from Denmark from an earlier paper by the same group:

denmark

800px-Saami_Family_1900pacnortWhen we think of peoples who aren’t farmers, we often think of marginalized nomadic or semi-nomadic groups. Many of the remaining hunter-gatherers such as Bushmen, as well societies which supplement their conventional lifestyle with a lot of hunting & gathering, such as the indigenous peoples of Siberia or the Sami of northern Scandinavia, occupy territory which is simply not viable for conventional agriculture. But this was not so in the past. Before the farmers arrived the rich bottom-lands were occupied by hunters & gatherers, of fish, game, grain, and nuts. In certain ecologies, such as around productive estuaries one could imagine enormous aggregations of these peoples. Additionally, it seems likely that a sedentary lifestyle predates farming. A good contemporary analog for what ancient Northern Europe may have been like was the Pacific Northwest before the European settlement. These native tribes were relatively affluent because of the abundance of salmon runs, and engaged in lavish signalling, such as with their famous potlatches. Seeing as how there are Atlantic salmon runs in places like Norway and Scotland one can make even closer correspondences perhaps!

Stonehenge-GreenAs I have stated before just because we have no written records of this period, we can not assume that these were necessarily the fragmented and scattered “small-scale societies” which we’re familiar with today. There may have been ideologically motivated political coalitions and alliances which broke down along ethnic and cultural lines. In the paper above the authors argue that there is evidence that a climatic constraint, crops which do not have a good yield in cooler or warmer temperatures, is a weak hypothesis. If so I wonder if it is a bit too pat to simply model the dynamics as a diffusive “bottom up” process. Seems plausible enough for much of Europe where Mesolithic populations were thin on the ground because of local carrying capacity, but I suspect that the encounter between dense agglomerations of farmers and fishermen resulted in an inevitable ramp up of political integration and consolidation, as villages and tribes had to coordinate together because of a positive feedback loop of conflict.

Image Credit: Lordkinbote, Mactographer

November 9, 2010

European man of many faces: Cain vs. Abel

UE-1

When it comes to the synthesis of genetics and history we live an age of no definitive answers. L. L. Cavalli-Sforza’s Great Human Diasporas would come in for a major rewrite at this point. One of the areas which has been roiled the most within the past ten years has been the origin and propagation of the agricultural lifestyle across the European continent between 10,000-6,000 years before the present (starting in Europe’s southeast fringe a few thousand years after the origination of the Neolithic lifestyle in the Levant, and finally pushing into the southern Scandinavian peninsula only ~6,000 years ago). The reasons for this particular debate about the origin of the European are manifold. First, most scholars are of European ancestry, and some of the debates have roots going back a century. So a natural interest exists based on normal human biases. Second, when it comes to genetics the climate of Europe is ideal for the preservation and extraction of ancient DNA. Third, there are relatively clear and distinct theoretical models which can be tested by the data, whether to verify or refute.

ResearchBlogging.orgI have already reviewed earlier work in three previous posts, European man perhaps a Middle Eastern farmer, European man perhaps not a Middle Eastern farmer, and Völkerwanderung back with a vengeance. Instead of rehashing everything I’ll take it as a given that you’ve read or skimmed those posts. Rather, let’s move on to a new paper in PLoS Biology, Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities:

In Europe, the Neolithic transition (8,000–4,000 B.C.) from hunting and gathering to agricultural communities was one of the most important demographic events since the initial peopling of Europe by anatomically modern humans in the Upper Paleolithic (40,000 B.C.). However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. To date, inferences about the genetic make up of past populations have mostly been drawn from studies of modern-day Eurasian populations, but increasingly ancient DNA studies offer a direct view of the genetic past. We genetically characterized a population of the earliest farming culture in Central Europe, the Linear Pottery Culture (LBK; 5,500–4,900 calibrated B.C.) and used comprehensive phylogeographic and population genetic analyses to locate its origins within the broader Eurasian region, and to trace potential dispersal routes into Europe. We cloned and sequenced the mitochondrial hypervariable segment I and designed two powerful SNP multiplex PCR systems to generate new mitochondrial and Y-chromosomal data from 21 individuals from a complete LBK graveyard at Derenburg Meerenstieg II in Germany. These results considerably extend the available genetic dataset for the LBK (n = 42) and permit the first detailed genetic analysis of the earliest Neolithic culture in Central Europe (5,500–4,900 calibrated B.C.). We characterized the Neolithic mitochondrial DNA sequence diversity and geographical affinities of the early farmers using a large database of extant Western Eurasian populations (n = 23,394) and a wide range of population genetic analyses including shared haplotype analyses, principal component analyses, multidimensional scaling, geographic mapping of genetic distances, and Bayesian Serial Simcoal analyses. The results reveal that the LBK population shared an affinity with the modern-day Near East and Anatolia, supporting a major genetic input from this area during the advent of farming in Europe. However, the LBK population also showed unique genetic features including a clearly distinct distribution of mitochondrial haplogroup frequencies, confirming that major demographic events continued to take place in Europe after the early Neolithic.

sommer-nadachowski-2006-figAs I’ve indicated before the archaeological jargon is rather mystifying to me. Some of this is due to translation, the Linear Pottery Culture is abbreviated “LBK” because in the German it is Linearbandkeramik. Rather, I try and focus on some basic concrete parameters: time and space. So we have the first agricultural society with a focus on Central Europe flourishing ~7,000 years before the present. Some now we have the time and space in mind around which we can bracket all the background variables. The big question being asked, and answered, is whether the practitioners of LBK were descendants of Ice Age Europeans who expanded from the “refugia” in the south of Europe during the Last Glacial Maximum (LGM) ~20,000 years ago. To speak intelligently about these issues you need some basic intuition, so you see the map which I found on John Hawks’ weblog showing the line of settlement during the LGM. As the ice retreated presumably the European hunter-gatherers would have rapidly pushed northward, following the species which they consumed.

I’ll pass over the methodological nuts & bolts; you can find them in the paper. Obviously this isn’t technically trivial; extracting, amplifying, and avoiding contamination, from DNA samples on the order of 7,000 years old is awesome. As usual they focused on mtDNA because this is found in much larger quantities than nuclear DNA. They did get a few Y chromosomal results though, though mtDNA is the star of the show here. The mtDNA is the maternal lineage, so it can tell you only so much. Additionally, there may be selection dynamics going on to change the frequencies of some of these variants. But with those caveats in hand I think mtDNA patterns can be very informative because if women are on the move that is a pointer to a classic folk-wandering, where a whole people transplant their culture via migration. Many more British women arrived in the New World than Spanish women, and therein lay one of the crucial factors in the difference between Anglo and Latin America.

The slide show below has all the major figures of interest. I’ve also replicated the full description, and made some minor edits. Please take in the table; much of the paper really presupposes an intuitive familiarity with mtDNA haplogroup frequencies.



mtDNA pairwise Fst by population
Hunter-Gatherers Near East LBK
Near East 4.46 * *
LBK 9.9 3.22 *
Central Europe 3.67 1 4.22

The authors also had an Fst table illustrating genetic distances using mtDNA of ancient and contemporary populations. I’ve cleaned up the table a bit, and standardized the values so that the smallest distance = 1. This is mostly so you can make immediate sense of it. What you clearly see is the enormous genetic distance between Central European hunter-gatherers and LBK, who were present in Germany right before the arrival of farmers. This comes very close to a falsification of the maximalist pots-not-people model, whereby farming spread from its point of origin in Anatolia and the Levant through a process of cultural diffusion, just like the alphabet or the potato. The relatively large distance between ancient and modern populations shouldn’t be too surprising, genetic distances operate across both time and space. There are interesting inferences one can make about the nature of gene flow over the past 10,000 years in Eurasia when viewing the relatively small distance between the two modern populations, but really the important point for the purposes of this paper is the high wall between the two cultures who practice differing modes of production.

In the paper the authors support, tentatively, a classic demic diffusion process. This is basically a very simple model whereby farmers with larger population growth rates expand into the “space” of hunter-gatherers. But as Dienekes Pontikos notes such a process would also be characterized by dilution of the original Middle Eastern “genetic signal” over time. Rather, what we see here seems to be a total transfer for a population across large distances. The authors themselves note that the LBK farmers seem to have followed the interior lines of rivers and flat-bottom plains. Farmers had discovered a new way to exploit nature, but in the end they were still ecologically constrained. The northern two-thirds of Scandinavia still had hunter-gatherer populations down to the period of the classical Greeks. This was not because of the powerful magic wielded by Väinämöinen. The Middle Eastern derived agricultural toolkit no doubt began to run into its natural ecological limits on Europe’s northern fringe. Without knowing anything further I suspect that the death of the southern Sami culture in the face of Norwegian and Swedish expansion in the early modern period was probably driven by the emergence of more systematic agricultural science, which could push the ecological limits beyond the long-standing equilibrium established in the Iron Age.

But I don’t think this is just a story of ecology. It is clearly a story of culture. We assume that culture is easily transferable from society to society. In some ways it is. The original phonetic script of Upper Mesopotamia and Syria seems to have quickly triggered imitation and appropriation from India to Italy within a few centuries of its widespread use by the Aramaeans. But farming is not like the idea of writing. The original farmers seem to have expanded rather slowly initially out of the Middle East. Not only did they perfect the biological character of their crops, they probably perfected the customs and traditions which would go along with farming. A complex suite of explicit rules and implicit norms. Perhaps it was not so easy to simply copy the farming lifestyle? Or, perhaps more interestingly, the hunter-gatherers by and large did not want to copy the farming lifestyle? (this is a tendency among some modern non-farming groups, who would rather work temporarily on farms themselves rather than become full-time obligate peasants) The large genetic distances between the LBK and the hunter-gatherers around them may indicate not only the relatively endogenous growth of the LBK in “virgin” land (e.g., compare to the Yankees of New England in the 17th and 18th century), but, also the emergence of an ideological aversion to mixing with the “savages.” We have plenty of textually attested de-humanization of the “savage” and “barbarian” by the “civilized.” It is likely that the gap between the LBK and the hunter-gatherers of Europe was only somewhat smaller than that between the Aborigines of Australia and Tasmania and the European settlers!

Finally, there’s one last issue I want to highlight: the authors find that many presumably hunter-gatherer lineages are found among the LBK, while very common haplogroups (mtDNA and Y) in Europe today are not found among the LBK or the ancient hunter-gatherers. The clear inference then would be that Europe went through several periods of demographic change and migration within the last 10,000 years. A simple two-way admixture scenario will not suffice. Yesterday I posted this bar plot which contrasted the pattern of ancestry of French vs. French Basque using ADMIXTURE at K = 10:

French

The green element is nearly 100% in Sardinia, and drops off to nearly nothing somewhere around Iran. The light blue component is modal around the Caucasus, though is widely distributed, from Spain to Bengal (yeah, that’s me!) to Sweden. A simple model would be that the light blue arrived with Neolithic agriculturalists, as the Basques are the descendants of the original Ice Age Europeans. But this may not be correct, and our impression of the Basques may be totally false. It is not out of the question now that the Basque culture may have arrived via the ancient leap-frogging of agriculture from fertile regions around the Mediterranean before the seafarers passed into the Atlantic and swept around the western fringe of Iberia. What we may be seeing is a palimpsest of agriculturalists, where the Basques simply lack the last layer.

In any case, one can speculate a lot right. Ancient DNA has allowed us to refute maximalist versions of pots-not-people, but has also overturned our ability to hold to simple robust models. In science you prefer parsimony, unless parsimony simply can’t explain the patterns at hand. I think we’re there at this point.

Citation: Wolfgang Haak, Oleg Balanovsky, Juan J. Sanchez, Sergey Koshel, Valery Zaporozhchenko, Christina J. Adler, Clio S. I. Der Sarkissian, Guido Brandt, Carolin Schwarz, Nicole Nicklisch, Veit Dresely, Barbara Fritsch, Elena Balanovska, Richard Villems, Harald Meller, Kurt W. Alt, Alan Cooper, & Genographic Consortium (2010). Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities PLoS Biology : 10.1371/journal.pbio.1000536

October 28, 2010

Sons of the conquerors: the story of India?

munda2

The past ten years has obviously been very active in the area of human genomics, but in the domain of South Asian genetic relationships in a world wide context it has seen veritable revolutions and counter-revolutions. The final outlines are still to be determined. In the mid-1990s the conventional wisdom was that South Asians were a branch of a broader West Eurasian cluster of peoples, albeit more distant from the core Middle Eastern-North-African-European-Caucasian clade. The older physical anthropological literature would have asserted that South Asians were predominantly Caucasoid, but with a Australoid element admixed in at varying proportions as a function of geography and caste. To put it more concretely, and I think accurately, a large degree of South Asian physical variety can be defined along the spectrum between A. R. Rahman and Nawaz Sharif. The regional and caste truisms are only correlations. Subrahmanyan Chandrasekhar was a Tamil Brahmin, but experienced anti-black racism in the United States. I think that is reasonable in light of his appearance.

ResearchBlogging.orgThis rough & ready mainstream understanding, supporting by classical genetic markers, was overturned in the early years of the 21st century. One line of thought argued that South Asians were much more distinctive from the broader Western Eurasian cluster of peoples. Representative of this body of work is a paper like The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. These researchers tended to start with the female lineages, mtDNA, and then supplement that with Y lineages, the paternal descent. A separate line of evidence, generally drawn from Y chromosomal results, indicated that there were deep connections between the people of India and those of Central Eurasia, in particular via the R1a haplogroup. Additionally, one aspect of the first set of results which was very surprising was that it actually placed South Asians closer to East, not West, Eurasians. But by the end of the aughts the uniparental studies had been supplemented by a range of results produced from SNP-chips, which looked at hundreds of thousands of genetic variants. These studies seemed to support the older view of South Asians being closer to West Eurasians than East Eurasians. Finally last year a paper came out which posited that almost all South Asian populations were actually an ancient stabilized hybrid between two groups, a European-like population, “Ancient North Indians” (ANI), and another group which is no longer present in unadmixed form, “Ancient South Indians” (ASI), of whom the Andaman Islanders are distant relatives. Though there was a slight bias toward ANI as a whole, the fraction of ASI increased as one went southeast, and down the caste ladder. The distinctive “South Asian” ancestral group in other words then may actually be conceived of as a compound of these two elements; an admixture of the native substrate against a European-like genetic background.

Strangely it sounds an awful lot like the older idea of a Caucasoid population with Australoid admixture. We know now that the connection between the tribal peoples of India, and the indigenous groups of South and Southeast Asia as a whole, to those of Australia and Melanesia, is tenuous at best. So the term “Australoid” is not really informative, and may even mislead. And in terms of historical linguistics I don’t think we’ve solved the problem by appealing to an “Aryan invasion.” The high fraction of ANI among South Indian tribal groups who are isolated from even Dravidian caste groups is a clue to the likelihood that the admixture event is very ancient, and probably precedes the arrival of the Aryans to the Indian subcontinent.

But there are more than two actors in this game. In Reconstructing Indian population history the authors acknowledge that their model is stylized, that reality is more complex. Additionally, they perceive in their data that some tribal groups from northeast India have an element which is outside of the purview of a two-way admixture event. They discarded this set from their broader analysis because this seemed to be a restricted phenomenon to these groups. A new paper in Molecular Biology and Evolution re-injects this third element into the picture. Population Genetic Structure in Indian Austroasiatic speakers: The Role of Landscape Barriers and Sex-specific Admixture:

The geographic origin and time of dispersal of Austroasiatic (AA) speakers, presently settled in South and Southeast Asia, remains disputed. Two rival hypotheses, both assuming a demic component to the language dispersal, have been proposed. The first of these places the origin of Austroasiatic speakers in Southeast Asia with a later dispersal to South Asia during the Neolithic, whereas the second hypothesis advocates pre-Neolithic origins and dispersal of this language family from South Asia. To test the two alternative models this study combines the analysis of uniparentally inherited markers with 610,000 common SNP loci from the nuclear genome. Indian AA speakers have high frequencies of Y chromosome haplogroup O2a; our results show that this haplogroup has significantly higher diversity and coalescent time (17-28 KYA) in Southeast Asia, strongly supporting the first of the two hypotheses. Nevertheless, the results of principal component and “structure-like” analyses on autosomal loci also show that the population history of AA speakers in India is more complex, being characterised by two ancestral components – one represented in the pattern of Y chromosomal and EDAR results, the other by mtDNA diversity and genomic structure. We propose that AA speakers in India today are derived from dispersal from Southeast Asia, followed by extensive sex-specific admixture with local Indian populations.

Some background is necessary here. South Asia is notoriously linguistically diverse, but, that diversity can be bracketed into several broad families. First, the Indo-European languages are represented by Indo-Aryan and Iranian dialects (and Germanic, if you include English). Second, the Dravidian languages are found across the subcontinent, from Brahui in Pakistan to Malto in Bangladesh. But they’re really the dominant languages in the southern cone of South Asia. That being said it seems likely that historically their distribution extended far into the north, with Brahui in western Pakistan being a relic of that period, as well as the fragmented tribal groups in Central India. There is also evidence down to historic periods of a Dravidian-speaking substrate in Maharashtra. And purely from a philological perspective it seems clear that many Indo-Aryan languages evolved within a Dravidian linguistic substrate.

Next, in the far north there are languages of Tibetan provenance and affinity. These are explicable in their origins and relationship. But in the northeast third of the Indian subcontinent there are a two groups of Austro-Asiatic languages. The prefix “Austro” is indicative of the symbiotic relationship between historical linguistics and physical anthropology in the early 20th century (most famously illustrated in the transplantation of the social-linguistic term Aryan from a South Asian and Iranian context, to a racialized Northern European term). The map at the top of this post shows the distribution of the Austro-Asiatic languages, as well as their subdivisions. There is clearly an eastern and western wing to the group, but most scholars assume that this is an artifact of the historical eruption of the Burman and Thai peoples out of the southern fringes of the Chinese Empire and into mainland Southeast Asia.

800px-Ramakrishna_Mission_Cherrapunjee_106Within India the Austro-Asiatic languages fall into two broad categories: the Munda and the Khasi. The Khasi inhabit the massif which separates Bengal and Assam. Their culture and society is at some variance from the norm in India (they are matrilocal, and animist or Christian). A close relationship to the people to the east is clear in both their language and their physical appearance. The Khasi, and other groups such as the Garo, are of the family of peoples and ethnicities which have arrived from the east and north relatively recently, making the transition from the world of Tibet and Burma to India. This is evident in the face of the Khasi child in the image to the left. Once passing out of their lands of origin these populations have assimilated to different degrees to the Indic domain. The Tripuri people for example retain a Tibeto-Burman language, but are adherents of Vaishnav Hinduism (my own family were once subjects of the Manikya dynasty). The Ahom of Assam were totally assimilated by the Indo-Aryan substrate. Like the Bulgars of Bulgaria their only influence was in the ethnonym that they contributed to their subjects. A quick survey of my own genetics, and those of other South Asians of eastern origin on 23andMe, clearly shows the influence of assimilated Tibeto-Burmans. One Bangladeshi Muslim individual clearly carries an East Asian Y chromosomal haplogroup.

The Munda are a somewhat different case. In older historical literature on South Asia there is some consideration that the Munda may be the earliest inhabitants of India; predating the Dravidians. Some readers of South Asian origin also point out that in the early Indo-Aryan language there may be more evidence of Munda, than Dravidian, influence. But the eastern connections of the Munda languages seem clear, albeit less explicable than those of the Khasi or the Tibeto-Burman peoples of the far northeast. If the Munda are the indigenous people then it stands to reason that the Mon-Khmer languages derive from South Asia. On the other hand the vast majority of the Austro-Asiatic languages exist in Southeast Asia, and, the Munda themselves have been hypothesized as being the bearers of rice-culture from the east.

This is where genetics comes into play. There has already been evidence of an eastern influence in the genes of the Munda from other researchers, so what this paper does is look at that in detail, instead of discarding it as a minor effect which muddles the broader picture. I’ve reformatted figure 3 to show how the groups relate to each other. On the left is a PCA. Most of the variance is west-east, ~6%, while some of it is north-south, ~1%. On the right is a bar plot generated from ADMIXTURE. I’ve edited out many of the populations. Focus on the Austro-Asiatic groups from India.

munda1

In the PCA you see the SE-NW axis of ANI-ASI admixture which is the primary aspect of genetic variation within South Asia. Numerically Dravidian and Indo-Aryan groups along this axis are the vast majority of South Asians. But the Munda and other Austro-Asiatic groups are not trivial; there are strong suggestions that the eastern Indo-Aryan groups, Oriya, Bengali, and Assamese, are to some extent shaped by influence from the Austro-Asiatic elements. The closer connection of the Khasi to East Asian populations is clear on the PCA. But the fact that the South Indian samples are further along axis-Y than the Munda are indicative of admixture in the Munda population. Looking at the bar plot that’s clear. The dominant dark-green signature of South Indian ancestry is also predominant among the Munda, and found at non-trivial amounts among Iranian, Khasi, and Southeast Asian populations, but the Munda clearly have an eastern component which is not found in South Indians. This is probably the element which perturbs them on the PCA.

But this just tells us the relationships in terms of total genome content. It doesn’t necessarily tells us the historical sequence of admixture events or the direction of migration. In fact the evidence of Indian ancestry in Southeast Asia could be suggesting migration from South Asia to the Southeast Asia (there is plenty of cultural evidence of transmission, though the presumption is that the demographic movements were marginal). They note in the paper that one phenomenon which could be obscuring and confusing our understanding is that much of gene flow occurs through isolation-by-distance (IBD). Village-to-village dynamics. In contrast to this you have folk wanderings, which result in a “leapfrog” aspect. The Hazara and Uyghur are both cases of leapfrogging, as their genetic makeup can’t be explained easily by IBD. So here the connections between the Munda and Southeast Asians, and the broader relationship between Southeast Asians and South Asians, could be IBD, or perhaps reflect deep ancient common ancestry. Perhaps the ASI group spanned the region from the Arabian Sea to the South China sea, and were only later overlain by ANI and East Asian populations.

To explore these questions the authors tunneled down to a more fine-grained scale, and looked at uniparental lineages as well as a gene at which recent selection seems to have operated upon East Asians in distinction to other groups, EDAR. Though uniparental lineages are only partially informative in terms of ancestry, they are very amenable to dating because of their haploid inheritance patterns. And the relationships between the branches of the termini can give us historical information.

The following figure shows the relationship and distribution of a particular Y chromosomal haplogroup which the Munda carry, and other South Asians tend not to, which connects them to the east:

munda3

The haplogroup is O2a (M95). The results from the Y chromosomal data are not clear, though they do seem to reject the model whereby Southeast Asian O2a lineages derive from Indian ones. But it does not seem as if you have a scenario where one founder lineage entered into South Asia from Southeast Asia, there are too many disparate branches of O2a found among Indians. Additionally, the coalescence time (back to last common ancestor) is deeper in Southeast Asia, but still deep in South Asia among the Munda. From this it seems that the origin of Austro-Asiatic languages in South Asia can be rejected, but the details of the emergence of Austro-Asiatic in South Asia can not be clearly perceived as of yet. From what I can gather the authors themselves do not necessarily believe that their results in this domain are robust (insensitive to varying the model’s assumptions even marginally).

An interesting point though is that the mtDNA, the female lineage, does not seem to diverge from other South Asians much at all. I find it intriguing that this is the same pattern we see along the major NW-SE axis of variation. It seems that mtDNA lineages unite South Asians, while the Y lineages separate them (by caste and region). The generality has many exceptions, but it points to a peculiar sex mediated admixture process from both the northwest and northeast. Men on the move have reshaped the genetics and culture of South Asia, but the mtDNA lineages still point to an ancient Eurasian group with distant but stronger affinities to the east than the west. The mtDNA are likely the purest distillation of ASI.

Finally, they look at frequencies of variants of EDAR among the South Asian groups. EDAR is in some ways diagnostic of East Asian ancestry; it seems that a variant which produces thick straight hair emerged relatively recently among East Asians.  Here’s the result from the HGDP browser:

edar1

edar2The G allele exhibits co-dominance, so the GA phenotype has intermediate hair-thickness between AA and GG. Haplotype structure based tests of natural selection have indicated that the derived G allele is recent. The map to the right shows the frequency of the derived G variant by population group. The bubble size is proportional to frequency, while the colors represent language groups. Again the Khasi and Tibeto-Burman groups are as you’d expect, they exhibit a relatively high frequency of the derived variant. The Hazara are a group which only came into being within the last 1,000 years through an admixture event. The Tharu seem to have their origins in Nepal’s transitional zone, and all the Nepali populations have significant admixture with Tibetan groups even if they themselves are not Tibetan in language and culture. The interesting result are the Munda. The Dravidian groups lack the derived EDAR variant, as do Indo-European groups without a plausible East Asian source of admixture. But within the Munda the derived variant is found in proportions ~5%. This is far lower than the 60% among the Tibeto-Burmans of the northeast, or the 40% among the Khasi, but it is significant. And this result allows the authors to reject the IBD model of connection for Austro-Asiatic groups, because the Munda harbor the variant which other South Asian groups in their environs do not. Gene flow predicated on linguistic affiliation at such a remove seems implausible, so the most parsimonious explanation is that the Munda languages arrived in India from Southeast Asia as part of a leapfrog folk wandering.

But why the low frequency of the derived variant? Obviously the Munda have admixed with the local substrate, so dilution would be one explanation. Another could be that when the Munda left East Asia the frequency was lower. Additionally, whatever selective forces were driving the frequency up may have abated in South Asia, and it could be that there was selection against the derived variant! Whatever the truth of it the existence of the derived EDAR variant among the Munda would be like finding the European LCT variant among an East Asian population: clear evidence of long distance gene flow and population movement.

So where does this lead us? First, let me observe that some of the authors on this paper are the same ones who argued for a predominantly indigenous origin for South Asians in the early 2000s based on mtDNA variation. In this paper they seem to be leaning against an indigenous origin for the Munda, or at least refuting the conjecture that the Munda are ur-Indians par excellence. I didn’t go into the details of the coalescence times because they’re rather a mess, but EDAR is probably a “tipping point” in arguing for a relatively recent exogenous origin for the Munda. The strong sex asymmetry in genetic variation is also suggestive, we have plenty of evidence of historical examples of genetic leapfrogs occurring through men-on-the-move. The asymmetry also seems to exist among the Khasi and other Tibeto-Burmans in India’s northeast (figure 2 of the paper).

The arguments about the history, culture, and genetics of South Asia have traditionally been disputed along the Aryan-Dravidian axis. I’m not interested in rehashing that aspect, but these data point us to another reality: on India’s northeast frontier there’s another component. As an ethnic Bengali myself I’ve always been somewhat aware of this. Some of my relatives and family acquaintances look much more like Garos than other South Asians. This component is even more evident on the face of Assamese and Nepali, whose languages are Indo-Aryan and religion is Hinduism, but whose appearance bespeaks a more variegated background. On some level South Asians from these regions are aware of their peculiarity, even if it isn’t spoken of much. I have read that in the wake of the victory of Japan over Russia in the early 20th century Bengali intellectuals expressed in public their pride at their Asiatic ancestry. With the rise of China in the 21st century I suspect more South Asians from Nepal, Bengal, and Assam, will rediscover that aspect of their background which links them to the east, and not the west. The genetics is just telling us what we already knew.

Citation: Gyaneshwer Chaubey, Mait Metspalu, Ying Choi, Reedik Mägi, Irene Gallego Romero, Pedro Soares, Mannis van Oven, Doron M. Behar, Siiri Rootsi, Georgi Hudjashov, Chandana Basu Mallick, Monika Karmin, Mari Nelis, Jüri Parik, Alla Goverdhana Reddy, Ene Metspalu, George van Driem, Yali Xue, Chris Tyler-Smith, Kumarasamy Thangaraj, Lalji Singh, Maido Remm, Martin B. Richards, Marta Mirazon Lahr, Manfred Kayser, Richard Villems, & Toomas Kivisild (2010). Population Genetic Structure in Indian Austroasiatic speakers: The Role of Landscape Barriers and Sex-specific Admixture Mol Biol Evol : 10.1093/molbev/msq288

Link acknowledgement: Dienekes Pontikos.

Addendum: This is more a speculative comment, so I will tack this on to the body of the main post. Here’s my current very tentative model for how South Asians came to be. At some point after the last Ice Age 10,000 years ago the ANI arrived, and hybridized with the ASI, who are descendants of the older original Out of Africa wave to South Asia. After this, but before the Aryans, the Munda arrived from the northeast, and pushed into lands inhabited by ANI-ASI groups. 4,000-3,000 years ago the Indo-Aryans arrive, and impose themselves as an elite on the ANI-ASI hybrid population, before being assimilated biologically and imparting their language to the Indian majority. I don’t know where Dravidian came from, but perhaps it was the language of the ANI (its existence in fragments all across the swath of the northern Indian subcontinent is suggestive, as well as possible connections to ancient Elamite, the language of Bronze Age southwest Iran). Eventually the Aryanized ANI-ASI marginalized the Munda in northeast India and drove them to the highlands. Finally, the Tibeto-Burmans arrived in the historical period.

Image Credit: Wikimedia Commons

September 12, 2010

The pristine Amazon – a zone of contention

Filed under: Amazon,Anthroplogy,Archaeology — Razib Khan @ 11:53 am

Mexico.Pue.Cholula.Pyramid.01Last week there was an article in The Washington Post that caught my eye, Scientists find evidence discrediting theory Amazon was virtually unlivable. The headline flattens a complex and roiling debate within academia. A generation ago the forests of the Amazon basin were seen as a pristine climax ecosystem. In the 1990s and 2000s that view started shifting, with the maximalist revisionisms recounted in Charles C. Mann’s 1491: New Revelations of the Americas Before Columbus. The general thesis is that the much of the Amazon was a managed ecosystem run for the benefit of a large population, but that the social systems collapsed under the weight of European diseases introduced after 1492. Naturally there are still some holdouts from the older paradigm who are deeply skeptical of the emerging consensus. From the article:

The number of scientists who disagree has diminished, but influential critics remain, none more so than Betty J. Meggers, director of Latin American archaeology at the Smithsonian Institution. She said the new theories are based more on wishful thinking than science.

“I’m sorry to say that archaeologists like to produce sensational refutation of previous theories,” said Meggers, whose 1971 book, “Amazonia: Man and Culture in a Counterfeit Paradise,” holds that the region is unfit for large-scale habitation. “You know, this is how you get your promotions.”


800px-Alto_orinoco5 (1)The main body of the piece is devoted to the revisionists who are probably transforming themselves into the new orthodox paradigm, and I can’t help but wonder if the reference to the date that Betty J. Meggers published her book is a sly allusion to Max Planck’s quip that “science advances one funeral at a time.” Meggers is correct insofar as scientific stardom comes through positive findings and paradigm shifts, and in interpretative fields such as archaeology the need to conform to particular ideological expectations can be strong. The archaeologists funded by Heinrich Himmler naturally glorified the material remains of ancient German societies (though Hitler was reputedly less than impressed with piles of pots). Similarly, one assumes that the very low estimates of Native American populations which were common before the 1980s in the United States had to do partly with the contention that North America was nearly empty when the Europeans arrived. Even if the influence was not conscious, it seems likely that it would have shaped interpretation, not to mention allocation of research funds. Who would give money to dig in regions where the assumption is that only hunter-gatherers had been resident before Europeans arrived on the scene? Today the shoe is on the other foot, and there is often a tendency to want to emphasize the achievements of non-Western peoples, and their equivalent complexity and civilizational attainment.

I think we need to see how things shake out over the next decade or so. My own general take here is conditioned by existence of the Maya civilization. If they had not left stone remains in the form of pyramids, written texts, and, if the late stages of their advanced culture had not been known to the Spaniards who conquered Mesoamerica, we might express skepticism at the idea that the Central American jungle could have produced any sort of high civilization at all. But civilizations have different propensities toward utilization of building materials which can stand the test of time. The Chinese have traditionally used materials which don’t preserve well, so that our knowledge of Chinese antiquity is more exclusively literary than is the case in the West, where great public buildings attest to the world of the ancients.

Note: if you’re interested in the archaeological debate, a good paper to start with: Amazonia 1492: Pristine Forest or Cultural Parkland?.

Image Credit: Wikimedia

August 31, 2010

The New World in three easy steps

Filed under: Anthroplogy,Archaeology,Human Expansion,New World,Paleoanthropology — Razib Khan @ 9:28 am

One aspect of human demographic expansions seems to be the fact that we often model them as a constant diffusion process, when in reality there were likely pulses (economic historians can conceive of this as the periodic gaps between land and labor factor inputs). I don’t know much about the human movements prior to H. sapiens sapiens, and from what I can gather the fossil remains are too sparse to be too wedded to a specific model, but it seems clear that anatomically modern human expansion occurred through a series of rapid outward sweeps which would periodically reach a “natural barrier.” Modern humans reached the Solomon Islands ~30,000 years ago, after which there was stasis for ~25,000 years. Only with the Austronesian expansion did humanity push past the Solomons. And this was no baby-step, ultimately the Austronesians went as far as the Hawaiian islands and Easter Island.


The New World is similar. The initial migration out of Africa by modern humans resulted in the range expansion of the human lineage into a region which had been untouched by earlier hominins, Australasia. But after that point tens of thousands of years passed before our species pushed into virgin territory, in this case North America. The when and the how of this though is still up for debate. A new paper PLoS One attempts to construct a plausible scenario by taking archaeological data points and inputing them into a diffusion model. Archaeological Support for the Three-Stage Expansion of Modern Humans across Northeastern Eurasia and into the Americas:

We use diffusion models…to quantify these dynamics. Our results show the expansion originated in the Altai region of southern Siberia ~46kBP , and from there expanded across northern Eurasia at an average velocity of 0.16 km per year. However, the movement of the colonizing wave was not continuous but underwent three distinct phases: 1) an initial expansion from 47-32k calBP; 2) a hiatus from ~32-16k calBP, and 3) a second expansion after the LGM ~16k calBP. These results provide archaeological support for the recently proposed three-stage model of the colonization of the Americas….Our results falsify the hypothesis of a pre-LGM terrestrial colonization of the Americas and we discuss the importance of these empirical results in the light of alternative models.

It’s an interesting paper because it seems to have been triggered in part by inferences made from the genetic data. I don’t know how confident archaeologists are about their radiometric dates, but I think some of the molecular clock results from the genetics of Amerindians need to be taken with a grain of salt (I don’t see many people repeating some of the really ancient coalescence dates for Amerindian Y lineages at this point).

These data seem to indicate that modern humans made it no further than previous hominin groups for several tens of thousands of years. But something happened within the last 20,000 years, and our species made the leap across Beringia. The bottleneck here is certainly not the Bering Strait, which was spanned by land much of the time in any case. Rather, our species didn’t have the biological or cultural capacity to survive in extremely frigid environments. I’ve read modern humans pushed the boundaries of their range in northern Europe further than Neandertals ever did, indicating our flexibility and plasticity. Since the human lineage had been resident in Eurasia for at least one million years that suggests to me that it was behavioral modernity that was key. In particular, how quickly our cultures evolve and shift. Though that flexibility itself may be a function of our biological competencies.

March 3, 2010

The temple that time forget

Filed under: Archaeology,Göbekli Tepe,History,Religion — Razib @ 2:51 pm

Aziz points me to a Newsweek article, History in the Remaking, on the Göbekli Tepe temple complex. The piece is a bit breathless:

Standing on the hill at dawn, overseeing a team of 40 Kurdish diggers, the German-born archeologist waves a hand over his discovery here, a revolution in the story of human origins. Schmidt has uncovered a vast and beautiful temple complex, a structure so ancient that it may be the very first thing human beings ever built. The site isn’t just old, it redefines old: the temple was built 11,500 years ago—a staggering 7,000 years before the Great Pyramid, and more than 6,000 years before Stonehenge first took shape. The ruins are so early that they predate villages, pottery, domesticated animals, and even agriculture—the first embers of civilization. In fact, Schmidt thinks the temple itself, built after the end of the last Ice Age by hunter-gatherers, became that ember—the spark that launched mankind toward farming, urban life, and all that followed.

A trivial point is that it was a spark at most, not the spark, as there are at least two independent sequences of the origination of agriculture leading to cities and the complex of cultural traits which we label “civilization.” A larger point is that I suspect it is incredible to us that hunter-gatherers could engage in such coordination because our model of what hunter-gatherers are capable of is constrained to Arctic peoples, the Bushmen and the Pygmies, and these populations are selection biased toward marginal lands which agriculturists were unable to exploit. In contrast, hunter-gatherers before agriculture were resident in much richer territory, and probably had more complex societies than we’re used to imagining. Probably something closer to the native populations of the North American Pacific Northwest.

On another issue, a friend who is like me a religious unbeliever wondered via email if Aziz’s jump to suggesting that Göbekli Tepe might be a glimpse into the first revelation was going a bit too far. I think the issue here is that Aziz, and many followers of the Abrahamic religions, simply start with different premises and so interpret these data through their own lens. His comment is open about his own perspective and how it colors his interpretation:

The relevance of this to faith is immense. If (as a believer, particularly of an Abrahamic faith) you accept the view that religion is a revelation from God to mankind, then the tempe at Göbekli Tepe really has potential to provide a meaningful narrative for that relationship. But the temple complex offers deep insights into human prehistory far beyond theological insights – it is a outlier in that a similar complex structure would not be built for five millenia later, in Iraq. It is such a mystery that the first archaeologist to discover it in the 60s was simply unable to process what he saw and walked away!

The bottom line is that with these temples, we see a glimpse of humanity at the cusp, not of civilization, but of understanding that there is more to existence than merely existing. The idea of the existence of the divine -the awakening from mere survival (post Ice Age) into a broader philosophical curiosity about why we are here and Who put us here – must have been like an ideological nuke to our forebears. It was literally Revelation, and perhaps it occurred there, at Göbekli Tepe , for the first time.

The idea that humanity began with a primal monotheism is not exclusive to Islam. Many conservative Christians, and I presume many Jews as well, accept this as a factual aspect of our species’ history. Adam and Noah were monotheists, and the panoply of religious traditions which were extant when Abrahamic monotheism began its meteoric rise is viewed from this perspective as degeneration from the original religion. The influence of initial framework is particularly stark when it comes to interpreting Mesopotamiam antiquities, conservative Christian friends of mine in high school saw in references to a flood in Sumerian mythology as validation of the Biblical story. That is, independent sources of confirmation of truths which they knew from revelation. In contrast, I inferred that these were in fact likely to be the source documents of the myths recorded in the Hebrew Bible.

But the second paragraph I have more issues with. I do not see in the existence of complex temples as any indication of philosophical theism. The Aztecs had complex temples, but they were manifestly barbaric, and arguably inhumane. If, for example, the excavators discovered human remains whose condition implied violent death and likely their sacrifice I assume Aziz would revise his assessment about the Göbekli Tepe complex. Or perhaps become a gnostic!

The full flower of philosophical reflection, and its synthesis with ethics and religion, is clear in the historical record, and goes by the term the Axial Age. It occurred on the order of 2,500 years ago. If it occurred at Göbekli Tepe it was lost to us in the interregnum. But I do not believe this is what happened, I suspect that the glimmers of such reflection, or at least the psychological atoms necessary to construct introspective philosophy and exploration of transcendence, has roots in behavioral modernity, on the order of 50,000 years ago (though I admit that my confidence in this is modest, and not high). In other words, I would bet that some humans were aware of their own mortality, and pondered their relation to the order of things, as they were leaving Africa. But only with the rise of complex societies which were open to sustainable rent-seeking could these humans transform their own personal reflections into the framework around which humanity ostensibly operated.

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January 19, 2010

Where are the “Paleolithic Europeans”?

Filed under: Archaeology,European genetics,Finn baiting — Razib @ 1:22 pm

Over at my other blog I have a review up of a new paper in PLoS Biology. The authors argue that a particular Y haplogroup lineage, R1b1b2, which has often been assumed to be a marker of indigenous Paleolithic Europeans (i.e., those who were extant before the rise of agriculture and the spread of farmers), is actually a signature of Anatolians who brough agriculture. This probably isn’t too surprising for the genetic genealogy nuts among the readers. After I got a copy of this paper I poked around the internet and the general finding that R1b1b2 was very diverse in the eastern Mediterranean seems to have been well known among the genetic genealogy community (also see Anatole Klyosov’s paper and what he says about Basques specifically). And then in eastern Europe you have R1a1, which seems to have also undergone recent range expansion. Finally, there are the recent rumblings out of ancient DNA extraction which imply a lot of turnover of mtDNA lineages during the shift from hunter-gathering to agriculture.

I think this makes us reconsider the idea that most of the ancestors of contemporary citizens of the European Union who were alive 10,000 years ago were actually resident within the current borders of the European Union. But let’s put the details of that aside for a moment. Which group might be most representative of Paleolithic Europeans? If the paper above is correct, the Basques are not a good proxy for the ancient hunter-gatherers of Europe.

Let’s look at a map which illustrates the spread of agriculture. I’d always focused on the SE-NW cline, but if the U5 mtDNA haplogroup is a reasonable marker of ancient pre-agricultural Europeans, we need to look at the Finnic peoples of the northeast. This may explain why these populations also tend to be genetically distinct from other European groups; not because they’re an exotic admixture, but because they’re not. Anyway, simply speculation, I’m sure readers will have their opinions….

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